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Subject: Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts
From: Reuti (reuti_at_[hidden])
Date: 2010-11-15 14:11:37


Just to give my understanding of the problem:

Am 15.11.2010 um 19:57 schrieb Terry Dontje:

> On 11/15/2010 11:08 AM, Chris Jewell wrote:
>>> Sorry, I am still trying to grok all your email as what the problem you
>>> are trying to solve. So is the issue is trying to have two jobs having
>>> processes on the same node be able to bind there processes on different
>>> resources. Like core 1 for the first job and core 2 and 3 for the 2nd job?
>>>
>>> --td
>>>
>> That's exactly it. Each MPI process needs to be bound to 1 processor in a way that reflects GE's slot allocation scheme.
>>
>>
> I actually don't think that I got it. So you give two cases:
>
> Case 1:
> $ qsub -pe mpi 8 -binding pe linear:1 myScript.com
>
> and my pe_hostfile looks like:
>
> exec6.cluster.stats.local 2
> batch.q_at_exec6.cluster.stats.local
> 0,1

Shouldn't here two cores be reserved for exec6 as it got two slots?

> exec1.cluster.stats.local 1
> batch.q_at_exec1.cluster.stats.local
> 0,1
> exec7.cluster.stats.local 1
> batch.q_at_exec7.cluster.stats.local
> 0,1
> exec5.cluster.stats.local 1
> batch.q_at_exec5.cluster.stats.local
> 0,1
> exec4.cluster.stats.local 1
> batch.q_at_exec4.cluster.stats.local
> 0,1
> exec3.cluster.stats.local 1
> batch.q_at_exec3.cluster.stats.local
> 0,1
> exec2.cluster.stats.local 1
> batch.q_at_exec2.cluster.stats.local
> 0,1
>
>
> Case 2:
> Notice that, because I have specified the -binding pe linear:1, each execution node binds processes for the job_id to one core. If I have -binding pe linear:2, I get:
>
> exec6.cluster.stats.local 2
> batch.q_at_exec6.cluster.stats.local
> 0,1:0,2
> exec1.cluster.stats.local 1
> batch.q_at_exec1.cluster.stats.local
> 0,1:0,2
> exec7.cluster.stats.local 1
> batch.q_at_exec7.cluster.stats.local
> 0,1:0,2
> exec4.cluster.stats.local 1
> batch.q_at_exec4.cluster.stats.local
> 0,1:0,2
> exec3.cluster.stats.local 1
> batch.q_at_exec3.cluster.stats.local
> 0,1:0,2
> exec2.cluster.stats.local 1
> batch.q_at_exec2.cluster.stats.local
> 0,1:0,2
> exec5.cluster.stats.local 1
> batch.q_at_exec5.cluster.stats.local
> 0,1:0,2
>
> Is your complaint really the fact that exec6 has been allocated two slots but there seems to only be one slot worth of resources allocated

All are wrong except exec6. They should only get one core assigned.

-- Reuti

> to it (ie in case one exec6 only has 1 core and case 2 it has two where maybe you'd expect 2 and 4 cores allocated respectively)?
>
> --
> <Mail-Anhang.gif>
> Terry D. Dontje | Principal Software Engineer
> Developer Tools Engineering | +1.781.442.2631
> Oracle - Performance Technologies
> 95 Network Drive, Burlington, MA 01803
> Email terry.dontje_at_[hidden]
>
>
>
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